Combine models into a model
It looks like Boolean doesn't work well because of overlapping faces. Maybe there's another to do it, but to merge 2 crossed Parallelepipeds, you could use the Tinycad addon:


Download the Tinycad addon: https://en.blender.org/index.php/Extensions:2.6/Py/Scripts/Modeling/mesh_tinyCAD
Enable it in your Preferences.
Select your whole mesh and press W > Tinycad > XALL/Intersect Selected Edges.
It has created some additional vertices on the crossing edges but it has also deleted faces.
Remove all the doubles with W > Remove Doubles.
Fill the faces with F.